GEO DataSets

(Submitter supplied) We previously reported that lifetime consumption of soy proteins or whey proteins reduced the incidence of azoxymethane (AOM)-induced colon tumors in rats. To obtain insights into these effects, global gene expression profiles of colons from rats with lifetime ingestion of casein (CAS, control diet), soy protein isolate (SPI), and whey protein hydrolysate (WPH) diets were determined. We identified 31 induced and 49 repressed genes in the proximal colons of the SPI-fed group and 44 induced and 119 repressed genes in the proximal colons of the WPH-fed group, relative to CAS. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS2468

Platform:

GPL85

9 Samples

Download data: CEL, EXP

Analysis of colons of soy or whey protein fed Sprague Dawley males 40 weeks after azoxymethane (AOM) injection to induce tumor formation. Lifetime consumption of soy or whey proteins reduces the incidence of AOM-induced colon tumors in rats.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL85

Series:

GSE6102

9 Samples

Download data: CEL, EXP

(Submitter supplied) The role of diet in the prevention of breast cancer is widely accepted, yet little is known on how early dietary effects mitigate adult cancer risk. Soy consumption is associated with reduced breast cancer risk in women, an effect largely attributed to the soy isoflavone genistein (GEN). We previously showed lower chemically-induced mammary tumor incidence in young adult rats with lifetime dietary intake of soy protein isolate (SPI), a highly refined soy product in infant formula, than in those fed the control diet Casein (CAS). more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS2616

Platform:

GPL341

10 Samples

Download data: CEL

Analysis of mammary epithelial cells of females fed a diet containing the soy isoflavone genistein or soy protein isolate. Soy consumption is associated with reduced breast cancer risk in women. Results provide insight into the molecular basis of the beneficial effect of soy-rich diets.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 3 protocol sets

Platform:

GPL341

Series:

GSE6879

10 Samples

Download data: CEL

(Submitter supplied) We have previously showed that whey protein hydrolysate (WPH) causes a greater increase in muscle protein synthesis than an identical composition of amino acids mixture does. The present study was conducted to investigate a comparative effect of WPH on gene expression. Male Sprague-Dawley rats subjected to a 2-h swimming exercise were administered either a carbohydrate-amino acid diet or a carbohydrate-WPH diet immediately after exercise. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS5390

Platform:

GPL1355

8 Samples

Download data: CEL

Analysis of epitrochlearis muscle from males exercised for 2hr then fed a whey protein hydrolysate (WPH) diet or a control diet with an identical amino acid composition (AAM). Results provide insight into the molecular basis of the greater post-exercise muscle protein synthesis in the WPH group.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, transformed count, 2 protocol sets

Platform:

GPL1355

Series:

GSE49486

8 Samples

Download data: CEL

(Submitter supplied) Beneficial effects of a soy diet on bone quality have been assumed to be due to the putative estrogenic actions of isoflavones. We studied the effects of soy protein isolate (SPI) on bone quality and compared these effects to 17β-estradiol (E2) in pre-pubertal rats. Female rats were weaned to a control diet with or without E2 (0.1, 1, 10 µg/kg/d), or SPI-containing diet with or without E2 (10 µg/kg/d) for 14 days beginning on postnatal day 20. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

12 Samples

Download data: CEL

(Submitter supplied) In order to properly understand whether xenoestrogens act as estrogens, it is essential to possess a solid portrait of the physiological effects of exogenous estradiol. Because the estrogen-dependent gene expression is one of the primary biomarkers of estrogenic action, we have assessed effects of three doses of exogenous estradiol (0.1, 1.0 and 10 µg/kg of body weight/day) on the mammary gland morphology and gene expression profiles by microarray analysis of prepubertal male and female rats of both sexes compared to untreated controls. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

24 Samples

Download data: CEL

(Submitter supplied) Soy foods have been suggested to have both positive health benefits and potentially adverse effects largely as a result of their content of isoflavone phytoestrogens. Since soy protein isolate (SPI) contains isoflavones, in addition to purported health benefits, safety concerns have been raised regarding the use of SPI and soy formulas, because of potential estrogenic actions during the neonatal period, including the potential for reproductive toxicity, infertility, and the possibility of increased risk for development and recurrence of estrogen sensitive cancers such as breast cancer. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL1355

12 Samples

Download data: CEL

(Submitter supplied) To understand how soy protein isolate (SPI) reduced liver steatosis in male obese Zucker rats, we conducted global gene expression (RNAseq) analysis on liver samples of male rats fed either the SPI or a control casein (CAS)-based diet (n=8 per group) for 16 wks. Bioinformatics was conducted using Ingenuity Pathway Analysis (IPA) software (Qiagen, CA) with P < 0.05 and 1.3 fold differential expression cutoff values.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22396

16 Samples

Download data: XLSX

(Submitter supplied) The linkage between nutrition and cancer prevention is an intriguing concept that is gaining widespread support based on epidemiological and animal studies. Multiple mechanisms likely underlie dietary protection against cancer, with effects influenced by target tissue response, cell-cell interactions and developmental context. Given the negative correlation between breast cancer incidence and intake of soy foods by Asian women, and the increasing consumption of soy protein-based formula by infants in the Western world, we have studied soy protein isolate (SPI) used in most infant formula as a paradigm to evaluate diet as a risk factor in a rodent model of mammary cancer. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL341

10 Samples

Download data: CEL

(Submitter supplied) In an effort to gain insight into the extensive dimension of post-translational modifications in histones (including H3K4me3 and H3K9ac) and elucidate the chemoprotective impact of dietary bioactive compounds on transcriptional control in a colon cancer preclinical model, we generated high-resolution genome-wide RNA (RNA-Seq) and “chromatin-state” (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed bioactive (i) fish oil (ii) butyrate (in the form of a fermentable fiber a rich source of SCFA), (iii) a combination of fish oil plus butyrate or (iv) control diets. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18694

107 Samples

Download data: XLS

(Submitter supplied) Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation. Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL6247

18 Samples

Download data: CEL, CHP

(Submitter supplied) Cocoa intake has been associated with health benefits, improving cardiovascular function and metabolism, as well as modulating intestinal immune function. The aim of this study was to take an in-depth look into the mechanisms affected by the cocoa intake by evaluating the colonic gene expression after nutritional intervention, and to ascertain the role of the fiber of cocoa in these effects. To achieve this, Wistar rats were fed for 3-weeks with either a reference diet, a diet containing 10% cocoa (C10), a diet based on cocoa fiber (CF) or a diet containing inulin (I). more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL14797

8 Samples

Download data: TXT

(Submitter supplied) mRNA used for the analysis of these microarrays were previously analyzed for 34 genes by reverse transcription - polymerase chain reaction in Desai BJ et al., J.Orthop.Trauma 17: 689-698, 2003. These two data sets were subsequently studied to compare the results from these two different methods for mRNA quantitation. The comparison was publised in "Comparison of mRNA gene expression by RT-PCR and DNA microarray" by W. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL85

10 Samples

Download data: CEL

(Submitter supplied) In order to characterize the changes in global gene expression in the distal colon of constipated SD rats in response to the laxative effects induced by aqueous extract of Liriope platyphylla (AEtLP) including isoflavone, saponin, oligosaccharide, succinic acid and hydroxyproline, total RNA extracted from the distal colon of AEtLP-treated constipation rats was hybridized to oligonucleotide microarrays.Overall, 581 genes were up-regulated and 216 genes were down-regulated by constipation induced by loperamide, while 67 genes were up-regulated and 421 genes were down-regulated by AEtLP treatment in constipated rats compared to controls. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL14746

3 Samples

Download data: XLS

(Submitter supplied) Goal: Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the longitudinal axis, contributes to a differential response to chemoprotective agents. Method: We assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. more...

Organism:

Rattus norvegicus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL14844

7 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Rattus norvegicus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL16371 GPL4135

22 Samples

Download data: TXT

(Submitter supplied) We have reported that microRNAs are present in human and bovine milk. But, it is unknown the roles of milk miRNAs. To clarify the roles of milk miRNAs, experimental animal such as rat study would be needed. However, it is unclear whether rat milk also contains miRNAs. Thus, we have employed microarray to show that rat milk also contains miRNAs.

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by array

Platform:

GPL16371

12 Samples

Download data: TXT

(Submitter supplied) We have reported that mRNAs are present in bovine milk. But, it is unknown the roles of milk mRNAs. To clarify the roles of milk mRNAs, experimental animal such as rat study would be needed. However, it is unclear whether rat milk also contains mRNAs. Thus, we have employed microarray to show that rat milk also contains mRNAs.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL4135

10 Samples

Download data: TXT